Humanity is continuing, the situation is bleak but I didn't see anything to indicate it isn't sustaining itself. Even in the ideal situation Ellie dies and somehow those three doctors with inadequate facilities can make progress towards a vaccine.
I've never understood what the next step is supposed to be. The amount of research required would be immense. Even supposing they DO find some miracle compound that can work as a vaccine which is easily identifiable... how do they manufacture it? I don't really see a mass production as feasible with the facilities as they are. Let alone the supply problems with whatever components are required
Sorry, but you're making up problems you have no evidence to prove exist. Lets say that science works differently in TLoU universe and they can produce it rather easily. I mean, it's not like wounds are depicted realistically, with Joel up and about at full ability only hours after taking some medicine after however many days of being bedridden after having an iron bar pierce his side. If that's possible, it's not too out there that the doctors are right and they can just whip up a vaccine with ellies brain like making scrabbled eggs.
And as far as the fireflies go, same thing. You have no idea what resources they have or don't have at their disposal. Or, even better, how do you know that once they have found a cure, other factions wouldn't offer their own resources in hopes of getting that cure? Humanity fell apart because it lost hope. It could fuck it up now that they recieved it again, but it's not an inevitability. Maybe the leaders of the factions see the opportunity they have to save the world and just give the fireflies what they need. I'm not saying they'll all hold hands and kumbaya, but they are under threat of extinction unless the vaccine gets made. It's possible they'll work together just for that part alone.
Let say they overcome that hurdle as well and manage to mass produce a vaccine. How do you distribute it? Hunters aren't going to suddenly stop what they are doing because the Fireflies have a vaccine and say we should all play nice now. The majority of humanity has reverted into an almost feral state - they aren't just going to come back.
Maybe they manage to smuggle it straight into the major remaining quarantine zones (we never even find out how many are remaining). I highly doubt the military is going to relax their grip on people at this point. Power corrupts, and they have absolute power.
Who cares? The argument you seem to be making now here is "We can't make people not be shitty, so whats the point?" Lets go with your scenerio, which frankly isn't unlikely. The world has been operating in a different way for 40 years and it will take generations to adjust in order for people to become somewhat civilized again.
So what? So we have a totalitarian regime for a couple centuries or however long while hunters continue being feralistic tribes. It's not a perfect societal existence, but all it means is that humanity just has to retread it's steps from where it used to be. We had totalitarian regimes aplenty, we're still going strong.
The point of the vaccine isn't to fix all of humanity's darker urges, it's to open the door to being rebuilt or atleast remove the possibility of extinction. That's it's only purpose, make it so humanity as a whole doesn't go extinct. If that results in the tyranny of one faction or another, well, that sucks, but that's humanity for you. It's not good, but it's not a threat to humanity, because tyrants are humans as much as the people they're oppressing. No matter how shitty things become, there is no threat to us as a species from ourselves. The virus is, however. I never expected the vaccine to be a magic fix for shitty people, just one that makes it so it's no longer afraid to retake the land it lost to the new dominant species.
Let's say the military is overcome with benevolence. It seems fairly few zones are still standing (speculation to be sure but it seems the most likely situation to me) but even if there are many. What's the next step? How, with little functional modern infrastructure, do you reestablish anything resembling a functioning government? How do you even gather the survivors, and if you do, how do you feed them until sustainability (ideally a farming season) can be achieved?
In the end, even if all the improbable situations required to produce and distribute this vaccine all come to be, I think you're left with a world of small colonies of survivors eking out a meager life in a very hostile world. We already have that. Clickers, runners and bloaters will still be out there, and they are going to kill you if they see you. I've yet to see the clicker who bit me once non-fatally and moved on. To me, immunity to spores and non-fatal bites isn't going to "save humanity".
Again, these are potential problems you have no evidence that even exist, except more unlikely. Having the resources to create, manufacture, and distribute the medicine feels atleast somewhat realistic, since not many people know how to make medicine. But
agriculture? That's relatively easy. There is no reason to think humanity doesn't have the resources to rebuild, because the only reason we are ever given why we can't go out into the open land is because "There be zombies"
If we can remove the threat of infection, you just need some decent police gear and all but the bloaters can't do shit to an armored group. The main threat lies in the fact that a single wound, however small, kills and then replenishes their number. Once you get rid of that, the zombies aren't a real threat. It doesn't matter how they don't give up trying to bite you if you have a decent set of riot gear protecting you. Combine that with some guns and ammunition, as well as a squad to watch your back, the zombies don't have a chance.
And once you do that, it's just a matter of making progress in terms of land use and establishing a government. And when I say that, I don't meant a benevolent government. Again, it's perfectly possible that we are looking at a militaristic totalitarian regime. That's fine. People will live under martial law for a couple generations, maybe they'll slowly dial back the fascism, or maybe it will take another bloody revolution. Again, that all sucks, but it's not a threat to humanity and it's how things have basically progressed for all recorded history of humanity. It's not good, but it's perfectly normal.
She knows where Joel is from, she knows some of the people he associated with. She may have even known Joel's brother from his time in the Fireflies. With her connections in Boston she would most likely have an easier time tracking him down then someone who know absolutely nothing about him.
Okay. Think about what your saying here.
You're suggesting that, to track joel she is going to go to Boston from Salt Lake City, which is
over 2000 miles away on the flimsy possibility that Joel is stupid enough to go somewhere that she could predict from talking to people he knows. Joel is unlikely to be going anywhere in particular, or if he is, it's probably unlikely to be somewhere that he knew he was known to go. He's effectively in hiding. He's not going anywhere where he is going to be recognized. There's no evidence that Marlene even knows Joel's brother, or do you think all fireflies know each other?
It's nothing short of ridiculous. Unless you're suggesting that Marlene is telepathic, she knows nothing about Joel that a complete stranger wouldn't. Even if what you said was true, the time it'd take to get to boston and then get back would give Joel such a head start that it wouldn't matter what information she got. THe only chance the fireflies had of realistically catching up to them is immediately, and they were going to try to do that regardless of whose in charge.